Perry L. Miller

Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis N. Marenco, Perry L. Miller, Gordon M. Shepherd, Kei-Hoi Cheung: Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. Artificial Intelligence in Medicine 48(1): 21-28 (2010)

Luis N. Marenco, Rixin Wang, Gordon M. Shepherd, Perry L. Miller: The NIF DISCO Framework: Facilitating Automated Integration of Neuroscience Content on the Web. Neuroinformatics 8(2): 101-112 (2010)

Kei-Hoi Cheung, Ernest Lim, Matthias Samwald, Huajun Chen, Luis N. Marenco, Matthew Holford, Thomas M. Morse, Pradeep Mutalik, Gordon M. Shepherd, Perry L. Miller: Approaches to neuroscience data integration. Briefings in Bioinformatics 10(4): 345-353 (2009)

Matthias Samwald, Ernest Lim, Peter Masiar, Luis N. Marenco, Huajun Chen, Thomas M. Morse, Pradeep Mutalik, Gordon M. Shepherd, Perry L. Miller, Kei-Hoi Cheung: Entrez Neuron RDFa: A Pragmatic Semantic Web Application for Data Integration in Neuroscience Research. MIE 2009: 317-321

Daniel Gardner, Huda Akil, Giorgio A. Ascoli, Douglas M. Bowden, William J. Bug, Duncan E. Donohue, David H. Goldberg, Bernice Grafstein, Jeffrey S. Grethe, Amarnath Gupta, Maryam Halavi, David N. Kennedy, Luis N. Marenco, Maryann E. Martone, Perry L. Miller, Hans-Michael Müller, Adrian Robert, Gordon M. Shepherd, Paul W. Sternberg, David C. Van Essen, Robert W. Williams: The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience. Neuroinformatics 6(3): 149-160 (2008)

Amarnath Gupta, William J. Bug, Luis N. Marenco, Xufei Qian, Christopher Condit, Arun Rangarajan, Hans-Michael Müller, Perry L. Miller, Brian Sanders, Jeffrey S. Grethe, Vadim Astakhov, Gordon M. Shepherd, Paul W. Sternberg, Maryann E. Martone: Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF). Neuroinformatics 6(3): 205-217 (2008)

Luis N. Marenco, Giorgio A. Ascoli, Maryann E. Martone, Gordon M. Shepherd, Perry L. Miller: The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers. Neuroinformatics 6(3): 219-227 (2008)

Luis N. Marenco, Yuli Li, Maryann E. Martone, Paul W. Sternberg, Gordon M. Shepherd, Perry L. Miller: Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework. Neuroinformatics 6(3): 229-239 (2008)

Chiquito J. Crasto, Luis N. Marenco, Nian Liu, Thomas M. Morse, Kei-Hoi Cheung, Peter C. Lai, Gautam Bahl, Peter Masiar, Hugo Y. K. Lam, Ernest Lim, Huajun Chen, Prakash M. Nadkarni, Michele Migliore, Perry L. Miller, Gordon M. Shepherd: SenseLab: new developments in disseminating neuroscience information. Briefings in Bioinformatics 8(3): 150-162 (2007)

Hugo Y. K. Lam, Luis N. Marenco, Tim Clark, Yong Gao, June Kinoshita, Gordon M. Shepherd, Perry L. Miller, Elizabeth Wu, Gwendolyn T. Wong, Nian Liu, Chiquito J. Crasto, Thomas M. Morse, Susie Stephens, Kei-Hoi Cheung: AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 8(S-3) (2007)

John Corwin, Avi Silberschatz, Perry L. Miller, Luis N. Marenco: Application of Information Technology: Dynamic Tables: An Architecture for Managing Evolving, Heterogeneous Biomedical Data in Relational Database Management Systems. JAMIA 14(1): 86-93 (2007)

Chiquito J. Crasto, Peter Masiar, Perry L. Miller: Case Report: NeuroExtract: Facilitating Neuroscience-oriented Retrieval from Broadly-focused Bioscience Databases Using Text-based Query Mediation. JAMIA 14(3): 355-360 (2007)

Mark Gerstein, Dov Greenbaum, Kei-Hoi Cheung, Perry L. Miller: An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective. Journal of Biomedical Informatics 40(1): 73-79 (2007)

Valentin Dinu, Hongyu Zhao, Perry L. Miller: Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis. Journal of Biomedical Informatics 40(6): 750-760 (2007)

Nian Liu, Fuqiang Xu, Perry L. Miller, Gordon M. Shepherd: OdorMapComparer: An Application for Quantitative Analyses and Comparisons of fMRI Brain Odor Maps. Neuroinformatics 5(2): 105-114 (2007)

Nian Liu, Luis N. Marenco, Perry L. Miller: Application of Information Technology: ResourceLog: An Embeddable Tool for Dynamically Monitoring the Usage of Web-Based Bioscience Resources. JAMIA 13(4): 432-437 (2006)

Nicholas Carriero, Michael V. Osier, Kei-Hoi Cheung, Perry L. Miller, Mark Gerstein, Hongyu Zhao, Baolin Wu, Scott Rifkin, Joseph T. Chang, Heping Zhang, Kevin White, Kenneth Williams, Martin H. Schultz: Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. JAMIA 12(1): 90-98 (2005)

Charles P. Friedman, Russ B. Altman, Isaac S. Kohane, Kathleen A. McCormick, Perry L. Miller, Judy G. Ozbolt, Edward H. Shortliffe, Gary D. Stormo, M. Cleat Szczepaniak, David Tuck, Jeffrey J. Williamson: White Paper: Training the Next Generation of Informaticians: The Impact of "BISTI" and Bioinformatics - A Report from the American College of Medical Informatics. JAMIA 11(3): 167-172 (2004)

Mark A. Shifman, Ranjana Srivastava, Cynthia Brandt, Tong-Ruei Li, Kevin White, Perry L. Miller: Case Report: Exploring the Portability of Informatics Capabilities from a Clinical Application to a Bioscience Application. JAMIA 11(4): 294-299 (2004)

Luis N. Marenco, Tzuu-Yi Wang, Gordon M. Shepherd, Perry L. Miller, Prakash M. Nadkarni: Model Formulation: QIS: A Framework for Biomedical Database Federation. JAMIA 11(6): 523-534 (2004)

Kei-Hoi Cheung, Janet Hager, Deyun Pan, Ranjana Srivastava, Shrikant Mane, Yuli Li, Perry L. Miller, Kenneth R. Williams: KARMA: a web server application for comparing and annotating heterogeneous microarray platforms. Nucleic Acids Research 32(Web-Server-Issue): 441-444 (2004)

Nian Liu, Fuqiang Xu, Luis N. Marenco, Fahmeed Hyder, Perry L. Miller, Gordon M. Shepherd: Informatics approaches to functional MRI odor mapping of the rodent olfactory bulb - OdorMapBuilder and OdorMapDB. Neuroinformatics 2(1): 3-18 (2004)

Luis N. Marenco, Nicholas P. Tosches, Chiquito J. Crasto, Gordon M. Shepherd, Perry L. Miller, Prakash M. Nadkarni: Application of Information Technology: Achieving Evolvable Web-Database Bioscience Applications Using the EAV/CR Framework: Recent Advances. JAMIA 10(5): 444-453 (2003)

Haseena Rajeevan, Michael V. Osier, Kei-Hoi Cheung, H. Deng, L. Druskin, R. Heinzen, Judith R. Kidd, S. Stein, Andrew J. Pakstis, Nick P. Tosches, C.-C. Yeh, Perry L. Miller, Kenneth K. Kidd: ALFRED: the ALelle FREquency Database. Update. Nucleic Acids Research 31(1): 270-271 (2003)

Peter Eckersley, Gary F. Egan, Erik De Schutter, Yiyuan Tang, Mirko Novak, Václav Sebesta, Line Matthiessen, Iiro P. Jääskeläinen, Ulla Ruotsalainen, Andreas V. M. Herz, K. Peter Hoffmann, Iiro P. Jaaskelainen, Stephen H. Koslow, Soo-Young Lee, Line Matthiessen, Perry L. Miller, Fernando Mira da Silva, Mirko Novak, Viji Ravindranath, Raphael Ritz, Ulla Ruotsalainen, Shankar Subramaniam, Arthur W. Toga, Shiro Usui, Jaap van Pelt, Paul F. M. J. Verschure, David Willshaw, Andrzej Wróbel, Yiyuan Tang: Neuroscience data and tool sharing - A legal and policy framework for neuroinformatics. Neuroinformatics 1(2): 149-165 (2003)

Chiquito J. Crasto, Luis N. Marenco, Michele Migliore, Buqing Mao, Prakash M. Nadkarni, Perry L. Miller, Gordon M. Shepherd: Text mining neuroscience journal articles to populate neuroscience databases. Neuroinformatics 1(3): 215-237 (2003)

Daniel Gardner, Arthur W. Toga, Giorgio A. Ascoli, Jackson T. Beatty, James F. Brinkley, Anders M. Dale, Peter T. Fox, Esther P. Gardner, John S. George, Nigel H. Goddard, Kristen M. Harris, Edward Herskovits, Michael L. Hines, Gwen A. Jacobs, Russell E. Jacobs, Edward G. Jones, David N. Kennedy, Daniel Y. Kimberg, John C. Mazziotta, Perry L. Miller, Susumu Mori, David C. Mountain, Allan L. Reiss, Glenn D. Rosen, David A. Rottenberg, Gordon M. Shepherd, Neil R. Smalheiser, Kenneth P. Smith, Tom Strachan, David C. Van Essen, Robert W. Williams, Stephen T. C. Wong: Towards effective and rewarding data sharing. Neuroinformatics 1(3): 289-295 (2003)

Cynthia Brandt, Richard Morse, Keri Matthews, Kexin Sun, Aniruddha M. Deshpande, Rohit Gadagkar, Dorothy B. Cohen, Perry L. Miller, Prakash M. Nadkarni: Metadata-driven creation of data marts from an EAV-modeled clinical research database. I. J. Medical Informatics 65(3): 225-241 (2002)

Mark A. Shifman, Frederick G. Sayward, Mark E. Mattie, Perry L. Miller: Case Study: Exploring Issues of Quality of Service in a Next Generation Internet Testbed: A Case Study Using PathMaster. JAMIA 9(5): 491-499 (2002)

Kei-Hoi Cheung, Janet Hager, Kenneth Nelson, Kevin White, Yuli Li, Michael Snyder, Kenneth R. Williams, Perry L. Miller: A dynamic approach to mapping coordinates between microplates and microarrays. Journal of Biomedical Informatics 35(5-6): 306-312 (2002)

Anuj Kumar, Kei-Hoi Cheung, Nick P. Tosches, Peter Masiar, Yang Liu, Perry L. Miller, Michael Snyder: The TRIPLES database: a community resource for yeast molecular biology. Nucleic Acids Research 30(1): 73-75 (2002)

Chiquito J. Crasto, Luis N. Marenco, Perry L. Miller, Gordon M. Shepherd: Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences. Nucleic Acids Research 30(1): 354-360 (2002)

Perry L. Miller, Prakash M. Nadkarni, Michael S. Singer, Luis N. Marenco, Michael L. Hines, Gordon M. Shepherd: Synthesis of Research: Integration of Multidisciplinary Sensory Data: A Pilot Model of the Human Brain Project Approach. JAMIA 8(1): 34-48 (2001)

Perry L. Miller: Application of Information Technology: Domain-constrained Generation of Clinical Condition Sets to Help Test Computer-based Clinical Guidelines. JAMIA 8(2): 131-145 (2001)

Perry L. Miller, Sandra J. Frawley, Frederick G. Sayward: Exploring the Utility of Demographic Data and Vaccination History Data in the Deduplication of Immunization Registry Patient Records. Journal of Biomedical Informatics 34(1): 37-50 (2001)

Perry L. Miller, Sandra J. Frawley, Frederick G. Sayward: Maintaining and Incrementally Revalidating a Computer-Based Clinical Guideline: A Case Study. Journal of Biomedical Informatics 34(2): 99-111 (2001)

Michael V. Osier, Kei-Hoi Cheung, Judith R. Kidd, Andrew J. Pakstis, Perry L. Miller, Kenneth K. Kidd: ALFRED: an allele frequency database for diverse populations and DNA polymorphisms - an update. Nucleic Acids Research 29(1): 317-319 (2001)

Kei-Hoi Cheung, Yang Liu, Anuj Kumar, Michael Snyder, Mark Gerstein, Perry L. Miller: An XML Application For Genomic Data Interoperation. BIBE 2001: 97-103

H. David Stein, Prakash M. Nadkarni, Joseph Erdos, Perry L. Miller: Research Paper: Exploring the Degree of Concordance of Coded and Textual Data in Answering Clinical Queries from a Clinical Data Repository. JAMIA 7(1): 42-54 (2000)

Mark E. Mattie, Lawrence H. Staib, Eric Stratmann, Hemant D. Tagare, James S. Duncan, Perry L. Miller: Research Paper: PathMaster: Content-based Cell Image Retrieval Using Automated Feature Extraction. JAMIA 7(4): 404-415 (2000)

Perry L. Miller: Viewpoint: Opportunities at the Intersection of Bioinformatics and Health Informatics: A Case Study. JAMIA 7(5): 431-438 (2000)

Roland Chen, Prakash M. Nadkarni, Luis N. Marenco, Forrest W. Levin, Joseph Erdos, Perry L. Miller: Research Paper: Exploring Performance Issues for a Clinical Database Organized Using an Entity-Attribute-Value Representation. JAMIA 7(5): 475-487 (2000)

Anuj Kumar, Kei-Hoi Cheung, Petra Ross-MacDonald, Paulo S. R. Coelho, Perry L. Miller, Michael Snyder: TRIPLES: a database of gene function in Saccharomyces cerevisiae. Nucleic Acids Research 28(1): 81-84 (2000)

Emmanouil Skoufos, Luis N. Marenco, Prakash M. Nadkarni, Perry L. Miller, Gordon M. Shepherd: Olfactory Receptor Database: a sensory chemoreceptor resource. Nucleic Acids Research 28(1): 341-343 (2000)

Kei-Hoi Cheung, Michael V. Osier, Judith R. Kidd, Andrew J. Pakstis, Perry L. Miller, Kenneth K. Kidd: ALFRED: an allele frequency database for diverse populations and DNA polymorphisms. Nucleic Acids Research 28(1): 361-363 (2000)

Prakash M. Nadkarni, Luis N. Marenco, Roland Chen, Emmanouil Skoufos, Gordon M. Shepherd, Perry L. Miller: Application of Information Technology: Organization of Heterogeneous Scientific Data Using the EAV/CR Representation. JAMIA 6(6): 478-493 (1999)

Emmanouil Skoufos, Matthew D. Healy, Michael S. Singer, Prakash M. Nadkarni, Perry L. Miller, Gordon M. Shepherd: Olfactory Receptor Database: a database of the largest eukaryotic gene family. Nucleic Acids Research 27(1): 343-345 (1999)

Prakash M. Nadkarni, Cynthia Brandt, Sandra J. Frawley, Frederick G. Sayward, Robin Einbinder, Daniel Zelterman, Lee Schacter, Perry L. Miller: Application of Technology: Managing Attribute-Value Clinical Trials Data Using the ACT/DB Client-Server Database System. JAMIA 5(2): 139-151 (1998)

S. Panzer, L. Cooley, Perry L. Miller: Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web. Computer Applications in the Biosciences 13(3): 281-290 (1997)

Susan E. Grajek, Pascal V. Calarco, Sandra J. Frawley, James McKay, Perry L. Miller, John A. Paton, Nancy K. Roderer, Joseph E. Sullivan: Research Paper: Evaluating IAIMS at Yale: Information Access. JAMIA 4(2): 138-149 (1997)

Prakash M. Nadkarni, Kei-Hoi Cheung, C. Castiglione, Perry L. Miller, Kenneth K. Kidd: DNA Workbench: A Database Package to Manage Regional Physical Mapping. Journal of Computational Biology 3(2): 319-329 (1996)

L. W. Wright, J. B. Lichter, John Reinitz, Mark A. Shifman, Kenneth K. Kidd, Perry L. Miller: Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty. Computer Applications in the Biosciences 10(4): 435-442 (1994)

Perry L. Miller, Prakash M. Nadkarni, P. A. Bercovitz: Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis. Computer Applications in the Biosciences 8(2): 141-147 (1992)

Perry L. Miller, Prakash M. Nadkarni, William R. Pearson: Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison. Computer Applications in the Biosciences 8(2): 167-175 (1992)

Perry L. Miller, Prakash M. Nadkarni, N. M. Carriero: Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm. Computer Applications in the Biosciences 7(1): 71-78 (1991)

Sheldon S. Ball, Vei H. Mah, Perry L. Miller: SENEX: a computer-based representation of cellular signal transduction processes in the central nervous system. Computer Applications in the Biosciences 7(2): 175-187 (1991)

Michael Factor, David Gelernter, Craig E. Kolb, Perry L. Miller, Dean F. Sittig: Real-Time Data Fusion in the Intensive Care Unit. IEEE Computer 24(11): 45-54 (1991)

Glenn D. Rennels, Edward H. Shortliffe, Frank E. Stockdale, Perry L. Miller: A Computational Model of Reasoning from the Clinical Literature. AI Magazine 10(1): 49-57 (1989)

Perry L. Miller, Glenn D. Rennels: Prose Generation from Expert Systems: An Applied Computational Linguistics Approach. AI Magazine 9(3): 37-44 (1988)

Perry L. Miller: Readings in Medical Artificial Intelligence: The First Decade (Book Review). AI Magazine 6(4): 105 (1986)

Perry L. Miller: ATTENDING: Critiquing a Physician's Management Plan. IEEE Trans. Pattern Anal. Mach. Intell. 5(5): 449-461 (1983)

Perry L. Miller: Medical Plan-Analysis: The Attending System. IJCAI 1983: 239-241